6B92

Crystal Structure of the N-terminal domain of human METTL16 in complex with SAH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H00 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52931.3 M K2HPO4, 45 mM NaH2PO4; drop contained 4 uL of protein solution (27 mg/mL) and 2 uL of reservoir solution; 0.2 uL of 200 mM SAM solution (buffered in 50 mM Hepes pH7.5) was added to the drop with mature crystals. 25% ethylene glycol was used for cryo-protection
Crystal Properties
Matthews coefficientSolvent content
4.7774.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 190.351α = 90
b = 190.351β = 90
c = 190.351γ = 90
Symmetry
Space GroupI 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15099.30.0640.066128.717.334224
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2395.91.361.410.72214.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2h002.144.8733194102799.340.1820.1810.219RANDOM54.009
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.476
r_dihedral_angle_4_deg18.363
r_dihedral_angle_3_deg15.232
r_long_range_B_refined7.766
r_long_range_B_other7.764
r_dihedral_angle_1_deg6.458
r_scangle_other4.606
r_mcangle_it3.498
r_mcangle_other3.496
r_scbond_other2.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.476
r_dihedral_angle_4_deg18.363
r_dihedral_angle_3_deg15.232
r_long_range_B_refined7.766
r_long_range_B_other7.764
r_dihedral_angle_1_deg6.458
r_scangle_other4.606
r_mcangle_it3.498
r_mcangle_other3.496
r_scbond_other2.842
r_scbond_it2.84
r_mcbond_it2.273
r_mcbond_other2.258
r_angle_refined_deg1.676
r_angle_other_deg1.016
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2113
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing